An outstanding goal in modern genomics is to systematically predict the functional outcome of noncoding variation associated with complex traits. To address this, we developed Hi-C-coupled multi-marker analysis of genomic annotation (H-MAGMA), which builds on traditional MAGMA—a gene-based analysis...
Functional characterization of pleiotropic variants The biological significance of these 100 independent pleiotropic variants (Supplementary Data 4–5) was evaluated using in silico annotation tools (Supplementary Data7)34,35,36. Pleiotropic variants were enriched in intergenic (P = 0.043) and non-c...
GO annotation enrichment analyses were conducted based on a Benjamini and Hochberg false discovery rate correction with significance set at p < 0.05 by using the Cytoscape plug-in BiNGO[26]. We mapped the sequence reads and contigs using SOAP http://soap.genomics.org.cn/soapaligner.html; ...
Contribution of cis Genetic Variation to Ancestry-Associated Transcriptional Variation, Related to Figure 4 (A) Enrichment of regulatory variants among pop-DE, pop-DR and genes that exhibit ancestry-associated differential isoform usage (pop-DIU). The enrichment factors are shown on the x axis in ...
Candidate gene discovery and annotation The significantly associated SNPs with flowering trait were searched for the orthologous sequences in genomes of otherVignaspecies as well as in other model crops. The putative candidate genes were identified using the BLASTx program from NCBI-BLAST (https://bl...
Further gene function annotation on the putative candidate genes were extremely significantly enriched in 31 GO terms (P < 0.01), including some BPs and MFs (Figure S5). In particular, numerous biosynthetic processes and metabolic processes were significantly enriched by some candidate genes, inc...
Variant annotation and impact prediction were performed with the SnpEff 4.3 program. Missense variants were further evaluated using several pathogenic prediction algorithms included in the dbNSFP v4.0 missense variant database and using the VarSome tool. Splicing variants were evaluated using the Human ...
Function annotation was completed by comparing BLAST v2.2.23 (http://blast.ncbi.nlm.nih.gov/Blast.cgi) results in M8 format to the Kyoto Encyclopedia of Genes and Genomes (KEGG) v59 [37], Cluster of Orthologous Groups of proteins (COG) v20090331 [27, 38], SwissProt v2011_10_19 [39...
--annotate_variation=./annotate_variation.pl The Annovar perl script of annotate_variation.pl -d humandb, --database_locat=humandb The database location/dir for the Annovar annotation datasets EXAMPLE ./InterVar.py -c config.ini # Run the examples in config.ini ./InterVar.py -b hg19 -i...
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005, 21: 3674-3676. 10.1093/bioinformatics/bti610. Article CAS PubMed Google Scholar Edgar RC: MUSCLE: mu...